Bioinformatics Pioneer, Martin Reese, on Scaling Up Human Genome Interpretation

Guest: Martin Reese, Co-founder, President & CSO, Omicia

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Chapters: (Advance the marker)

0:40 How did you get started in bioinformatics?

3:04 What is the biggest challenge with human genome interpretation?

8:01 Diagnosing Ogden Syndrome

13:30 What sets Omicia apart?

18:08 Who is ordering your tests?

23:29 FDA letter to 23andMe unfortunate

25:47 What's your main objective for 2014?

Martin Reese's career in bioinformatics began in 1993 when he attended a lecture in Heidelberg, Germany entitled "Genome Informatics." Reese, a German, then switched his studies from medical informatics to bioinformatics and moved to Berkeley where he worked on assembling the genome for the Human Genome Project. In 1996, he started a company with his Ph D advisor, David Haussler (of Genome Browser fame), called Neomorphic, part of the first commercialization of bioinformatics.

Martin is now the president of Omicia, a company he founded to take on the challenge of scaling up human genome interpretation.

How far have we come in the clinical interpretation space? Martin says that in 2013, 80% of human genome interpretation was done for research and 20% for the clinic. In the next 3-5 years, he predicts those percentages will switch to 20% for research and 80% clinical.

Martin says that one of the biggest challenges for human genome interpretation is easy-to-use visualization tools. For this reason, he's been a fan of the DTC company, 23andMe, and felt that the FDA's letter to the company was "very unfortunate."

"[23andMe] educated the whole population about genetics," he says in the interview, "and they tried to make the reports easily understandable and manageable by a regular person. . . . The easier we make the reports, the better doctors can understand them."

Just who is ordering reports from Omicia, and what is the company's objective in the year ahead? Join us for an insider's take on clinical genomics.

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Dietrich Hauffe of QIAGEN on Clinical NGS


Dietrich Hauffe, Sr. VP, Life Sciences, QIAGEN

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Listen (3:26) What is the big vision for QIAGEN?

Listen (2:26) Business already 50 percent clinical

Listen (3:15) Will NGS replace PCR in clinic?

Listen (6:01) What can you tell us about the GeneReader?

Listen (4:38) Where are we at with genome interpretation?

Listen (5:11) How is QIAGEN's relationship with clinical labs evolving?

QIAGEN is a company on the move. Last year they picked up two bioinformatics platforms, CLC Bio and Ingenuity Systems. They bought Intelligent Biosystems the year before. That purchase was for a new next generation sequencing device. Called the GeneReader, this instrument has been designed specifically for clinical application.

Joining us today is Dietrich Hauffe, the Sr. Vice President of Life Sciences at QIAGEN. Dietrich discusses the GeneReader, which is currently being tested by select customers, and how it fits into QIAGEN's big vision for genomic medicine. The GeneReader offers clinical technicians the ability to do parallel sequencing and to have "random access" to many samples at the same time. The GeneReader will not be able to do whole genome or exome sequencing, however.

Dietrich says that the GeneReader, along with QIAGEN's broad existing product line of sample prep, PCR tests, companion diagnostics, bioinformatics offerings, puts QIAGEN in a unique position in the clinical market. By owning the entire workflow, QIAGEN is in a position to raise the quality and standards in clinical testing.

"We're very much liked for our universal approach," Dietrich says in the interview.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

The Clinical Sequencer

A Feburary 7th article in the online version of Nature magazine began with the line, "Genomics finally came of age as a clinical discipline on November 19, 2013, when the US Food and Drug Administration (FDA) approved Illumina's MiSeqDx next-generation sequencing (NGS) system for clinical use."   

Now, some may argue with this and say genomics was coming of age with the BRCA test from Myriad back in the nineties, or with the use of NGS for cancer treatment, or the rise of prenatal diagnostics.

A New Gold Standard for Accuracy in NGS: Mike Hunkapiller, PacBio


Mike Hunkapiller, CEO, Pacific Biosciences

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Listen (4:58) What is the theme for 2014 at PacBio?

Listen (2:50) Are you working on a clinical sequencer?

Listen (6:55) What are your thoughts on regulation and diagnostics?

Listen (3:12) What was your reaction to the Oxford Nanopore data just released at AGBT?

Listen (6:40) PacBio runs becoming the gold standard in microbial sequencing

Mike Hunkapiller, the CEO of Pacific Biosciences, joins us again this year as part of our annual series on NGS. Last year, Mike stressed the importance of PacBio's SMRT(TM) sequencing to do longer reads than the competition--namely Illumina. He says PacBio will continue to stay focused on further improving read length and accuracy this year as well. In fact, he says that the PacBio technology is becoming "the new gold standard" for microbial sequencing.

What does Mike think of the first data released by Oxford Nanopore recently? And what are PacBio's plans for clinical sequencing? Join us in the second installment of NGS 2014.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

Illumina Dominates NGS with Still Much Room for Improvement


Shawn Baker, Chief Scientific Officer, AllSeq

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Listen (3:39) #AGBT14: to tweet or not to tweet

Listen (6:23) Illumina solidifies dominance

Listen (6:07) The Wizard of Oxford?

Listen (4:21) Qiagen with a killer workflow

Listen (2:21) Genapsys teases

Listen (1:07) Affy founder with a new technology

Listen (2:26) Aw shucks - a new reference genome

Listen (4:49) Where to from here?

Today we begin our annual sequencing series with Shawn Baker, Chief Scientific Officer at AllSeq.

In today's interview Shawn links highlights of last week's AGBT conference with the overall trends in the sequencing space. If last year was all about "long read" technology, Shawn says this year is about Illumina's total domination.

Yet there are newcomers. Qiagen is set to introduce a sequencer designed for clinical use. After picking up bioinformatics platforms, CLC Bio and Ingenuity last year, "Qiagen will have the workflow, start-to-finish, that no one else has these days," says Shawn.

The upstart Genapsys, funded by the Russian tech investor Yuri Milner, presented at AGBT with a teaser on their new sequencer with the footprint of an iPad. And Affymetrix founder, Steve Fodor, introduced a new company with a product that will integrate with NGS.

It's one of the hottest technologies in our business, and Shawn, who maintains an up-to-date Knowledge Bank at, can talk about it like no one else. Presenting NGS 2014.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

5 Myths of Genomic Medicine

No topic has been more popular at Mendelspod than that of genomic medicine.  This is partly an editorial decision.  But it also comes to us from every direction.  And it is very exciting to hear stories of new knowledge about human biology being translated into precision healthcare.  We have featured the major players in the NGS tools industry and some of the newcomers working on “next next gen”.  We’ve featured data analytics companies and some of the new genomic interpretation and reporting groups who are setting up shop.  We have interviewed professors talking about their latest discover

2013 'State of NGS' with Shawn Baker, BlueSEQ

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

. . . and by Biotix - makers of A BETTER TIP(TM) for Next Gen Sequencing


Shawn Baker, CSO, BlueSEQ Bio and Contact Info

Listen (9:29) The year of steady boring progress

Listen (4:44) PacBio has made impressive improvements

Listen (3:47) Nabsys and the gospel of long reads

Listen (4:29) Moleculo technology still unknown

Listen (4:55) Has sequencing technology reached a more stable plateau?

Listen (2:13) Illumina has a history of bumping heads with their customers

Formerly with Illumina, Shawn Baker is now CSO of BlueSEQ and a consultant on matters to do with next gen sequencing. He joins us for the second time to give an overview of the NGS industry. We caught up with Shawn just after AGBT where the industry players announce their latest and greatest.

Baker calls 2013 "the year of steady boring progress." Noting that there were not any huge breakthroughs, he says in fact there were some big promises made last year which have not been delivered on. However there has been progress, most notably by the steady improvements made to the PacBio system, and by the emergence into the field of companies such as BioNano Genomics and Nabsys focused on long read technology. What is Shawn's take on the gospel of long reads? And what does he think of the new Illumina/Moleculo technology? Join us for the State of NGS 2013.

Nabsys Close to Product Launch: CEO, Barrett Bready

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

. . . and by Biotix - makers of A BETTER TIP(TM) for Next Gen Sequencing


Barrett Bready , CEO, Nabsys Bio and Contact Info

Listen (5:44) Will Nabsys be the first to deliver a nanotech based sequencer?

Listen (7:11) Timeline for product release

Listen (2:13) Renewed focus on long reads

Listen (1:57) Thoughts on Moleculo

If there was a darling at this year's AGBT (and the genomics community has come to expect them), the spot would go to Nabsys, who presented their "positional" sequencer that employs nano detectors in a single-molecule approach. In today's interview, Nabsys CEO, Barrett Bready says he was surprised by the response to his new sequencer at the show and said many of those watching the machine work in real time expressed their desire to purchase the machine. Bready, who strikes me as quite modest even though he's sitting on what could be a game changer, says the company will be ready to commercially launch the product for around $50K in the second half of the year.

Bready talks about a major theme of last week's AGBT meeting and a theme we've been focusing on in this series: a renewed focus on long reads. "A relatively small number of us have been talking about the importance of structural variation and context and the ability to do de novo assembly for a while, and I think its now becoming mainstream in the genomics community. It's like real estate, location matters," he says in the interview.

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